DOCSLIB.ORG

And Trans-Acting Expression Quantitative Trait Loci Differentially Regulate Gamma-Globin Gene Expression

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
And Trans-Acting Expression Quantitative Trait Loci Differentially Regulate Gamma-Globin Gene Expression bioRxiv preprint doi: https://doi.org/10.1101/304899; this version posted April 20, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Cis- and Trans-Acting Expression Quantitative Trait Loci Differentially Regulate Gamma- Globin Gene Expression Elmutaz M. Shaikho1, 2, John J. Farrell1, David H. K. Chui1, Paola Sebastiani3, Martin H. Steinberg1 1Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA 2Bioinformatics Program, Boston University, Boston, MA 02215, USA 3Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA Acknowledgments: Funded in part by R01 HL 068970, RC2 HL 101212, R01 87681 (MHS), T32 HL007501 (EMS), from the NIH Bethesda, MD. Conflict-of-interest disclosure: The authors declare no competing interests. Correspondence: Martin H. Steinberg, 72 E. Concord St., Boston, MA 02118, 617-414-1020, FAX 617- 414-1021; [email protected] Contribution: PS, JJF, DHKC, MHS supervised the research and edited the paper, EMS conceived the the research, performed the analysis, and wrote the paper. Keywords: g-globin, fetal hemoglobin, eQTLs, BCL2L1, globin gene expression bioRxiv preprint doi: https://doi.org/10.1101/304899; this version posted April 20, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. ABSTRACT Genetic association studies have detected two trans-acting quantitative trait loci (QTL) on chromosomes 2, 6 and one cis-acting QTL on chromosome 11 that were associated with fetal hemoglobin (HbF) levels. In these studies, HbF was expressed as a percentage of total hemoglobin or the number of erythrocytes that contain HbF (F-cells). As the g-globin chains of HbF are encoded by two non-allelic genes (HBG2, HBG1) that are expressed at different levels we used normalized gene expression and genotype data from The Genotype-Tissue Expression (GTEx)-project to study the effects of cis- and trans-acting HbF expression or eQTL. This allowed us to examine mRNA expression of HBG2 and HBG1individually. In addition to studying eQTL for globin genes we examined genes co-expressed with HBG1, studied upstream regulators of HBG1 co-expressed genes and performed a correlation analysis between HBG2 and HBG1 and known HbF regulators. Our results suggest differential effect of cis and trans-acting QTL on HBG and HBG1 expression. Trans-acting eQTLs have the same magnitude of effect on the expression of both HBG2 and HBG1 while the sole cis-acting eQTL affected only HBG2. Furthermore, the analysis of upstream regulators and the correlation analysis suggested that BCL2L1 might be a new potential trans- acting HbF activator. HbF is the major modulator of the phenotype of sickle cell anemia and b thalassemia. Depending on the effect size, modification of trans-acting elements might have a greater impact on HbF levels than cis-acting elements alone. bioRxiv preprint doi: https://doi.org/10.1101/304899; this version posted April 20, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Introduction Genome-wide and other genetic association studies have detected many single nucleotide polymorphisms (SNPs) in chromosomes 2, 6, and 11 that were associated with fetal hemoglobin (HbF) levels in normal individuals and in patients with sickle cell anemia and b thalassemia (Thein et al. 1987; Craig et al. 1996; Garner et al. 1998; Uda et al. 2008; Mtatiro et al. 2014). These studies used either HbF protein levels-expressed as a percentage of total hemoglobin- or the percentage of all erythrocytes that had HbF detected by immunofluorescence (F-cells) as a quantitative trait. HbF is a tetramer composed of two a and two g-polypeptide subunits. The g-globin subunits, which characterize HbF, are encoded by two closely linked genes-from 5’ to 3’, HBG2 and HBG1 (together, HBG). The respective polypeptides of the g-globin genes differ by only a single amino acid in position 136; glycine in the Gg chain (HBG2) and alanine in the Ag chain (HBG1) (Schroeder et al. 1968). In adults, these genes are expressed at a ratio of 2:3 (Terasawa et al. 1980). Expression quantitative trait loci (eQTLs) are genomic loci that lead to variability in mRNAs expression levels and can be identified by analyzing global RNA expression using the expression levels of genes as quantitative phenotypes. Differential expression of HBG in whole blood can be detected by mRNA analysis that may provide an understanding of whether eQTL associated with HBG affects the expression of one or both genes. RNA sequence data (RNA-seq) and whole genome sequences from primary erythroid progenitors expressing HBG would provide the ideal data set to study cis and trans-acting elements that regulate HbF expression. However, such data are rarely available publicly. The Genotype-Tissue Expression (GTEx)- project provides an alternative resource to study HBG gene expression, the regulatory elements of these genes and the effects of genetic variation of these elements (GTEx_Consortium 2013). GTEx was launched in 2010 to create a publicly available database of genotype and tissue expression. Samples come from either deceased or surgical donor’s organ/tissues. These human tissue samples then undergo RNA- seq and genome-wide SNP analysis. The tissues sampled include peripheral blood, which contains bioRxiv preprint doi: https://doi.org/10.1101/304899; this version posted April 20, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. reticulocytes that express hemoglobin genes. Reticulocytes account for about 10% of total hemoglobin synthesis. We performed a genome-wide association study (GWAS) to detect eQTLs associated with expression of HBG in whole blood, other genes of the b-globin (HBB) gene cluster and with known HbF cis- and trans- acting regulators. In addition, we examined genes co-expressed with HBG1 to discover enriched pathways, studied upstream regulators of HbF co-expressed genes and performed correlation analysis between HBG and known HbF regulators. A similar correlation analysis included BCL2L1, a potential HbF activator we found in our analysis. We hypothesized that trans-acting elements that are transcription factors affect the expression of both HBG2 and HBG1, while the known cis-acting QTL in the promoter of HBG2 is likely to be associated with the expression of this gene only. Results Preliminary studies GTEx whole blood RNA-seq data detected HbF eQTLs in BCL11A, HMIP and in the HBB gene cluster using HbF gene expression as a surrogate for HbF protein levels, validating the utility of this data set for examining HbF-associated eQTL (Table 1 and Fig. 1A-F). Gene Symbol Variant Id SNP P-Value Effect Size T-Statistic Standard Error HBG1 2_60718043_T_G_b37 rs1427407 1.20E-11 -0.46 -7.1 0.065 HBG1 11_5263683_C_T_b37 rs10128556 0.89 -0.0085 -0.14 0.059 HBG1 6_135419018_T_C_b37 rs9399137 2.20E-15 0.51 8.4 0.061 HBG2 2_60718043_T_G_b37 rs1427407 1.10E-09 -0.46 -6.3 0.073 HBG2 11_5263683_C_T_b37 rs10128556 2.60E-16 0.51 8.7 0.058 HBG2 6_135419018_T_C_b37 rs9399137 1.70E-09 0.44 6.2 0.07 Table 1. SNPs from previous GWAS and their association with HBG1 and HBG2 expression in whole blood samples available in the GTEx portal. bioRxiv preprint doi: https://doi.org/10.1101/304899; this version posted April 20, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Figure 1. Effect of rs1427407 (2:60718043_T/G), rs10128556 (11:5263683_C/T), and rs9399137 (6:135418632_TTAC/T) on HBG1 and HBG2 expression in GTEx data set version 6. P-values are above genome-wide significance for rs1427407 (BCL11A, chr2) and rs9399137 (MYB, chr6) association with expression of both HBG genes. Rs10128556 (chr 11) is significantly associated with only HBG2 (p- bioRxiv preprint doi: https://doi.org/10.1101/304899; this version posted April 20, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. value of 2.60E-16) while it has no effect on HBG1(p-value 0.89) Het denotes heterozygous, and Homo, homozygous. Genome-wide eQTL association analysis Twenty-seven SNPs were eQTL associated with HBG1 (p-value ≤ 5 × 10−8). Of these 27, 21 were intergenic variants in the HMIP region on chromosome 6p, five were BCL11A variants on chromosome 2p, and one was on chromosome 11p (Fig. 2A, Table S1). The SNP rs66650371, the functional 3-bp deletion in the MYB enhancer, is one of the most significant SNPs in the HMIP region. The most significant SNP of the five BCL11A variants was rs1427407, which in other studies was the functional SNP in the erythroid-specific enhancer of this gene (Bauer et al. 2013). Forty-nine SNPs meeting genome-wide significance levels were eQTL for HBG2. Seventeen were intergenic variants in the HMIP region on chromosome 6, five were BCL11A variants on chromosome 2p, 26 were on chromosome 11p (Fig 2B, Table S2) and one was on chromosome 1.
Load more

Recommended publications
  • RBP-J Signaling − Cells Through Notch Novel IRF8-Controlled
    Sca-1+Lin−CD117− Mesenchymal Stem/Stromal Cells Induce the Generation of Novel IRF8-Controlled Regulatory Dendritic Cells through Notch −RBP-J Signaling This information is current as of September 25, 2021. Xingxia Liu, Shaoda Ren, Chaozhuo Ge, Kai Cheng, Martin Zenke, Armand Keating and Robert C. H. Zhao J Immunol 2015; 194:4298-4308; Prepublished online 30 March 2015; doi: 10.4049/jimmunol.1402641 Downloaded from http://www.jimmunol.org/content/194/9/4298 Supplementary http://www.jimmunol.org/content/suppl/2015/03/28/jimmunol.140264 http://www.jimmunol.org/ Material 1.DCSupplemental References This article cites 59 articles, 19 of which you can access for free at: http://www.jimmunol.org/content/194/9/4298.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on September 25, 2021 • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2015 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Sca-1+Lin2CD1172 Mesenchymal Stem/Stromal Cells Induce the Generation of Novel IRF8-Controlled Regulatory Dendritic Cells through Notch–RBP-J Signaling Xingxia Liu,*,1 Shaoda Ren,*,1 Chaozhuo Ge,* Kai Cheng,* Martin Zenke,† Armand Keating,‡,x and Robert C.
    [Show full text]
  • Microglia Emerge from Erythromyeloid Precursors Via Pu.1- and Irf8-Dependent Pathways
    ART ic LE S Microglia emerge from erythromyeloid precursors via Pu.1- and Irf8-dependent pathways Katrin Kierdorf1,2, Daniel Erny1, Tobias Goldmann1, Victor Sander1, Christian Schulz3,4, Elisa Gomez Perdiguero3,4, Peter Wieghofer1,2, Annette Heinrich5, Pia Riemke6, Christoph Hölscher7,8, Dominik N Müller9, Bruno Luckow10, Thomas Brocker11, Katharina Debowski12, Günter Fritz1, Ghislain Opdenakker13, Andreas Diefenbach14, Knut Biber5,15, Mathias Heikenwalder16, Frederic Geissmann3,4, Frank Rosenbauer6 & Marco Prinz1,17 Microglia are crucial for immune responses in the brain. Although their origin from the yolk sac has been recognized for some time, their precise precursors and the transcription program that is used are not known. We found that mouse microglia were derived from primitive c-kit+ erythromyeloid precursors that were detected in the yolk sac as early as 8 d post conception. + lo − + − + These precursors developed into CD45 c-kit CX3CR1 immature (A1) cells and matured into CD45 c-kit CX3CR1 (A2) cells, as evidenced by the downregulation of CD31 and concomitant upregulation of F4/80 and macrophage colony stimulating factor receptor (MCSF-R). Proliferating A2 cells became microglia and invaded the developing brain using specific matrix metalloproteinases. Notably, microgliogenesis was not only dependent on the transcription factor Pu.1 (also known as Sfpi), but also required Irf8, which was vital for the development of the A2 population, whereas Myb, Id2, Batf3 and Klf4 were not required. Our data provide cellular and molecular insights into the origin and development of microglia. Microglia are the tissue macrophages of the brain and scavenge dying have the ability to give rise to microglia and macrophages in vitro cells, pathogens and molecules using pattern recognition receptors and in vivo under defined conditions.
    [Show full text]
  • Roles and Regulation of Transcription Factor Mafa in Islet Β-Cells
    Endocr. J./ S. ARAMATA et al.: INSULIN TRANSCRIPTION AND MafA doi: 10.1507/endocrj.KR-101 REVIEW Roles and Regulation of Transcription Factor MafA in Islet β-cells * SHINSAKU ARAMATA, SONG-IEE HAN AND KOHSUKE KATAOKA Graduate School of Biological Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan ＊Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba Science City, Ibaraki 305-8572, Japan. Released online August 30, 2007 Correspondence to: Kohsuke KATAOKA, Graduate School of Biological Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan Abstract. Insulin is a critical hormone in the regulation of blood glucose levels. It is produced exclusively by pancreatic islet β-cells. β-cell-enriched transcription factors, such as Pdx1 and Beta2, have dual roles in the activation of the insulin gene promoter establishing β-cell-specific insulin expression, and in the regulation of β-cell differentiation. It was shown that MafA, a β-cell-specific member of the Maf family of transcription factors, binds to the conserved C1/RIPE3b element of the insulin promoter. The Maf family proteins regulate tissue-specific gene expression and cell differentiation in a wide variety of tissues. MafA acts synergistically with Pdx1 and Beta2 to activate the insulin gene promoter, and mice with a targeted deletion of mafA develop age-dependent diabetes. MafA also regulates genes involved in β-cell function such as Glucose transporter 2, Glucagons-like peptide 1 receptor, and Prohormone convertase 1/3. The abundance of MafA in β-cells is regulated at both the transcriptional and post-translational levels by glucose and oxidative stress.
    [Show full text]
  • Differential Expression of Vitamin D Binding Protein in Thyroid Cancer Health Disparities
    www.oncotarget.com Oncotarget, 2021, Vol. 12, (No. 7), pp: 596-607 Research Paper Differential expression of Vitamin D binding protein in thyroid cancer health disparities Brittany Mull1, Ryan Davis2,3, Iqbal Munir4, Mia C. Perez5, Alfred A. Simental6 and Salma Khan2,3,6,7 1Harbor UCLA Medical Center, Torrance, CA 90502, USA 2Division of Biochemistry, Loma Linda, CA 92350, USA 3Center for Health Disparities & Molecular Medicine, Loma Linda, CA 92350, USA 4Riverside University Health System, Moreno Valley, CA 92555, USA 5Department of Pathology & Human Anatomy, Loma Linda University School of Medicine, Loma Linda, CA 92354, USA 6Department of Otolaryngology, Loma Linda University School of Medicine, Loma Linda, CA 92354, USA 7Department of Internal Medicine, Loma Linda University School of Medicine, Loma Linda, CA 92354, USA Correspondence to: Salma Khan, email: [email protected] Keywords: DBP; thyroid cancer; health disparities Received: November 16, 2020 Accepted: March 05, 2021 Published: March 30, 2021 Copyright: © 2021 Mull et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT Thyroid cancer incidence, recurrence, and death rates are higher among Filipino Americans than European Americans. We propose that vitamin D binding protein (DBP) with multifunctionality with ethnic variability plays a key role within different ethnicities. In this study, we determined the correlation between differential DBP expression in tumor tissues and cancer staging in Filipino Americans versus European Americans. We assayed DBP expression by immunohistochemistry and analyzed the data with confocal microscopy on 200 thyroid cancer archival tissue samples obtained from both ethnicities.
    [Show full text]
  • Prox1regulates the Subtype-Specific Development of Caudal Ganglionic
    The Journal of Neuroscience, September 16, 2015 • 35(37):12869–12889 • 12869 Development/Plasticity/Repair Prox1 Regulates the Subtype-Specific Development of Caudal Ganglionic Eminence-Derived GABAergic Cortical Interneurons X Goichi Miyoshi,1 Allison Young,1 Timothy Petros,1 Theofanis Karayannis,1 Melissa McKenzie Chang,1 Alfonso Lavado,2 Tomohiko Iwano,3 Miho Nakajima,4 Hiroki Taniguchi,5 Z. Josh Huang,5 XNathaniel Heintz,4 Guillermo Oliver,2 Fumio Matsuzaki,3 Robert P. Machold,1 and Gord Fishell1 1Department of Neuroscience and Physiology, NYU Neuroscience Institute, Smilow Research Center, New York University School of Medicine, New York, New York 10016, 2Department of Genetics & Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, 3Laboratory for Cell Asymmetry, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan, 4Laboratory of Molecular Biology, Howard Hughes Medical Institute, GENSAT Project, The Rockefeller University, New York, New York 10065, and 5Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 Neurogliaform (RELNϩ) and bipolar (VIPϩ) GABAergic interneurons of the mammalian cerebral cortex provide critical inhibition locally within the superficial layers. While these subtypes are known to originate from the embryonic caudal ganglionic eminence (CGE), the specific genetic programs that direct their positioning, maturation, and integration into the cortical network have not been eluci- dated. Here, we report that in mice expression of the transcription factor Prox1 is selectively maintained in postmitotic CGE-derived cortical interneuron precursors and that loss of Prox1 impairs the integration of these cells into superficial layers. Moreover, Prox1 differentially regulates the postnatal maturation of each specific subtype originating from the CGE (RELN, Calb2/VIP, and VIP).
    [Show full text]
  • Temporal Mapping of CEBPA and CEBPB Binding
    Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Temporal mapping of CEBPA and CEBPB binding during liver regeneration reveals dynamic occupancy and specific regulatory codes for homeostatic and cell cycle gene batteries Janus Schou Jakobsen1,2,3,*, Johannes Waage1,2,3,4, Nicolas Rapin1,2,3,4, Hanne Cathrine Bisgaard5, Fin Stolze Larsen6, Bo Torben Porse1,2,3,* 1 The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, DK2200 Copenhagen, Denmark; 2 Biotech Research and Innovation Centre (BRIC), University of Copenhagen, DK-2200 Copenhagen, Denmark; 3 The Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, DK2200 Copenhagen Denmark; 4 The Bioinformatics Centre, University of Copenhagen, DK2200, Copenhagen, Denmark; 5 Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, DK- 2100 Copenhagen, Denmark; 6 Department of Hepatology, Rigshospitalet, DK2200 Copenhagen, Denmark. JW: [email protected]; NR: [email protected]; HCB: [email protected]; FSL: [email protected] * Corresponding authors: BTP: [email protected]; JSJ: [email protected], The Finsen Laboratory, Ole Maaløesvej 5, Copenhagen Biocenter, University of Copenhagen, DK2200 Copenhagen, Denmark. Telephone: +45 3545 6023 Running title: Regulation of liver regeneration Keywords: Temporal ChIP-seq, dynamic binding, liver regeneration, C/EBPalpha, C/EBPbeta, transcriptional networks 1 Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract Dynamic shifts in transcription factor binding are central to the regulation of biological processes by allowing rapid changes in gene transcription.
    [Show full text]
  • Transcriptional Control of Microglia Phenotypes in Health and Disease
    REVIEW SERIES: GLIA AND NEURODEGENERATION The Journal of Clinical Investigation Series Editors: Marco Colonna and David Holtzmann Transcriptional control of microglia phenotypes in health and disease Inge R. Holtman,1,2 Dylan Skola,1 and Christopher K. Glass1,3 1Department of Cellular and Molecular Medicine, UCSD, San Diego, California, USA. 2Department of Medical Physiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands. 3Department of Medicine, UCSD, San Diego, California, USA. Microglia are the main resident macrophage population of the CNS and perform numerous functions required for CNS development, homeostasis, immunity, and repair. Many lines of evidence also indicate that dysregulation of microglia contributes to the pathogenesis of neurodegenerative and behavioral diseases. These observations provide a compelling argument to more clearly define the mechanisms that control microglia identity and function in health and disease. In this Review, we present a conceptual framework for how different classes of transcription factors interact to select and activate regulatory elements that control microglia development and their responses to internal and external signals. We then describe functions of specific transcription factors in normal and pathological contexts and conclude with a consideration of open questions to be addressed in the future. Introduction regulatory control necessary to generate cell type–specific programs Microglia are tissue-resident macrophages that perform CNS- of gene expression. This additional information is provided by distal specific functions (1). They derive from a unique lineage of eryth- regulatory elements called enhancers (12). Enhancers represent the romyeloid precursors (EMPs) in the yolk sac and fetal liver (2). most numerous binding sites for LDTFs and signal-dependent tran- EMPs infiltrate the brain during early development, differentiate scription factors (SDTFs), and are major sites for the integration of into microglia, and maintain their population by self-renewal (3).
    [Show full text]
  • Calculating the Statistical Significance of Rare Variants Causal for Mendelian and Complex Disorders
    bioRxiv preprint doi: https://doi.org/10.1101/103218; this version posted January 25, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Calculating the statistical significance of rare variants causal for Mendelian and complex disorders Aliz R Rao1*, Stanley F Nelson1,2,3† *Correspondence: [email protected] †Email: [email protected] 1Department of Human Genetics, University of California, Los Angeles, Los Angeles, California, USA. 2Department of Psychiatry and Biobehavioral Sciences at the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA. 3Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California, USA. 1 bioRxiv preprint doi: https://doi.org/10.1101/103218; this version posted January 25, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract With the expanding use of next-gen sequencing (NGS) to diagnose the thousands of rare Mendelian genetic diseases, it is critical to be able to interpret individual DNA variation. We developed a general method to better interpret the likelihood that a rare variant is disease causing if observed in a given gene or genic region mapping to a described protein domain, using genome-wide information from a large control sample.
    [Show full text]
  • LPS Induces the Degradation of Programmed Cell Death Protein 4
    THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 289, NO. 33, pp. 22980–22990, August 15, 2014 © 2014 by The American Society for Biochemistry and Molecular Biology, Inc. Published in the U.S.A. LPS Induces the Degradation of Programmed Cell Death Protein 4 (PDCD4) to Release Twist2, Activating c-Maf Transcription to Promote Interleukin-10 Production* Received for publication, April 10, 2014, and in revised form, June 27, 2014 Published, JBC Papers in Press, June 30, 2014, DOI 10.1074/jbc.M114.573089 Mirjam W. M. van den Bosch‡1, Eva Palsson-Mcdermott‡, Derek S. Johnson§, and Luke A. J. O’Neill‡ From the ‡School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland and the §Department of Pathology and Laboratory Medicine, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104 Background: LPS-induced PDCD4 degradation leads to IL-10 induction. Results: LPS-induced PDCD4 degradation results in release of Twist2, resulting in c-Maf induction and IL-10 production. Conclusion: The PDCD4/Twist2 interaction has an important anti-inflammatory role in LPS signaling. Significance: This study reports the mechanism of PDCD4/Twist2 interaction and provides a new insight of IL-10 production Downloaded from via suppression of PDCD4/Twist2 interaction. Programmed cell death protein 4 (PDCD4) is a tumor sup- ent complexes, mTOR complex 1 (mTORC1) and mTORC2. pressor and has also been shown to suppress production of the mTORC1 comprises mTOR in a complex with mLST8 http://www.jbc.org/ immunomodulatory cytokine IL-10. The precise role of PDCD4 (mammalian lethal with SEC13 protein 8), PRAS40 (proline- in IL-10 induction in macrophages is still not fully understood.
    [Show full text]
  • The Basic Motif-Leucine Zipper Transcription Factor Nrl Can
    Proc. Natl. Acad. Sci. USA Vol. 93, pp. 191-195, January 1996 Genetics The basic motif-leucine zipper transcription factor Nrl can positively regulate rhodopsin gene expression (retinal genes/retinal diseases/maf oncogene family/DNA-binding protein) ALNAWAZ REHEMTULLA*t, RON WARWARt, RAJAN KUMAR§, XIAODONG Jlt, DONALD J. ZACK§P, AND ANAND SWAROOPt,* *,tt *Howard Hughes Medical Institute and Departments of tOphthalmology and **Human Genetics, W. K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI 48105; and Departments of §Ophthalmology, 1Molecular Biology and Genetics, and liNeurosciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287 Communicated by James V. Neel, University of .Michigan Medical School, Ann Arbor, MI, August 31, 1995 ABSTRACT The retinal protein Nrl belongs to a distinct the bZIP family of DNA-binding proteins (14). It is highly subfamily of basic motif-leucine zipper DNA-binding proteins conserved between mouse and man and demonstrates a retina- and has been shown to bind extended AP-1-like sequence specific pattern of expression on Northern analysis (11, 13). elements as a homo- or heterodimer. Here, we demonstrate The Nrl protein shows strong sequence homology to the v-maf that Nrl can positively regulate the expression of the photo- oncogene product (15). Maf and Nrl define a distinct subfamily receptor cell-specific gene rhodopsin. Electrophoretic mobil- of bZIP proteins that includes the c-mafprotooncogene prod- ity-shift analysis reveals that a protein(s) in nuclear extracts uct (16), several other Maf proteins (17, 18), the small subunit from bovine retina and the Y79 human retinoblastoma cell p18 of the erythroid transcription factor NF-E2 (19), and the line binds to a conserved Nrl response element (NRE) in the product of the segmentation gene kriesler (kr) (20).
    [Show full text]
  • Mafa Enables Pdx1 to Effectively Convert Pancreatic Islet Progenitors and Committed Islet A-Cells Into B-Cells in Vivo
    Diabetes Volume 66, May 2017 1293 Mafa Enables Pdx1 to Effectively Convert Pancreatic Islet Progenitors and Committed Islet a-Cells Into b-Cells In Vivo Taka-aki Matsuoka,1 Satoshi Kawashima,1 Takeshi Miyatsuka,1,2 Shugo Sasaki,1 Naoki Shimo,1 Naoto Katakami,1 Dan Kawamori,1 Satomi Takebe,1 Pedro L. Herrera,3 Hideaki Kaneto,4 Roland Stein,5 and Iichiro Shimomura1 Diabetes 2017;66:1293–1300 | DOI: 10.2337/db16-0887 Among the therapeutic avenues being explored for re- including coronary and renal disease. A variety of innova- placement of the functional islet b-cell mass lost in tive approaches are being explored to produce b-cells from type 1 diabetes (T1D), reprogramming of adult cell types embryonic stem cells (1,2) and adult cell types (3–5). A into new b-cells has been actively pursued. Notably, supposition in these efforts involves producing conditions mouse islet a-cells will transdifferentiate into b-cells un- that correctly regulate the transcription factor networks der conditions of near b-cell loss, a condition similar to required in programming pancreatic progenitor cells into ISLET STUDIES a T1D. Moreover, human islet -cells also appear to poised b-cells and subsequently controlling mature islet cell func- for reprogramming into insulin-positive cells. Here we tion. These include transcription factors like Pdx1 (6–10), have generated transgenic mice conditionally expressing which is essential in the formation of early pancreatic ep- the islet b-cell–enriched Mafa and/or Pdx1 transcription ithelium, developing b-cells and adult islet b-cells, as well factors to examine their potential to transdifferentiate as neurogenin 3 (Ngn3) (11–13), which is required during embryonic pan–islet cell Ngn3-positive progenitors and embryogenesis for specification of all islet cell types (i.e., the later glucagon-positive a-cell population into b-cells.
    [Show full text]
  • University of Cincinnati
    UNIVERSITY OF CINCINNATI Date: 5/8/06 I, Emily E. Bosco Hereby submit this work as part of the requirements for the degree of: Doctor of Philosophy in: Cell and Molecular Biology It is entitled: RB Modifies the Therapeutic Response of Breast Cancer This work and its defense approved by: Chair: Erik Knudsen Sue Heffelfinger Kathy Hepner-Goss Sohaib Khan Yolanda Sanchez The Retinoblastoma Tumor Suppressor Modifies the Therapeutic Response of Breast Cancer A dissertation submitted to the Division of Research and Advanced Studies of the University of Cincinnati in partial fulfillment of the requirements for the degree of Doctorate of Philosophy (Ph.D.) in the Department of Cell Biology, Neurobiology, and Anatomy of the College of Medicine 5/8/06 by Emily Elizabeth Bosco B.S. University of Notre Dame, 2001 Committee Chairman: Erik S. Knudsen Ph.D. Abstract: The retinoblastoma tumor suppressor (RB) is functionally inactivated in the majority of human cancers, and nearly half of all breast cancers. Here, we investigate the consequence of RB loss on the response to DNA damage and anti-estrogenic therapies used in the treatment of breast cancer. Initially, we demonstrate that downstream RB targets are severely mis-regulated following acute deletion in adult primary cells causing abrogation of the DNA damage checkpoint and consequently, accumulation of secondary DNA lesions upon treatment with chemotherapeutics. Additionally, we found that RB modifies the DNA repair response in adult primary fibroblasts, such that RB-deficient cells are able to repair UV-induced lesions at an accelerated rate. These initial studies reveal that RB loss in primary cells modifies the response to DNA damage by promoting aberrant replication and inappropriately accelerating repair, both of which may ultimately sensitize cells to DNA damaging therapies.
    [Show full text]